Improving homebrewing with the help of arduinos and XOD: Our Biomaker Challenge

We are a small, merry band of newbie Biomakers and amateur homebrewers and have started a project to monitor the progression of our fine brews in real time. By day we are two research scientists and a Biology teacher.

 We are looking to develop a piece of kit which allows us to see how quickly our homebrew is turned from a mixture of sugars in the initial malty extract into alcohol in beer. As sugars are converted to alcohol by the yeast, the density, or Specific Gravity (SG), of the liquid decreases and this is traditionally monitored by the means of a hydrometer. The SG decreases over time until it reaches a final plateau, at which point all of the sugars have been turned into alcohol. We are interested in monitoring how quickly this happens and how we can monitor it in real time.

Sam’s Biomaker Starter Kit arrives “what an exciting package to find on my desk first day back in the lab in 2019!”

An alcohol meter, testing beer immediately after brewing but before fermentation.

Image by Jeena on Wikipedia, shared under CC BY-SA 3.0

Getting started…

Initial challenges

As two of us have absolutely no prior knowledge of using Arduinos the first challenge has been to work out which end of the lead plugs into the laptop and which end into the Arduino. One of us has much more experience of programming, but not huge experience with Arduinos. It’s pretty much a ragtag skillset, held together with a Whatsapp group, copious mugs of tea, soup, swearing and an overarching dedication to the cause of better homebrew.

Initial thoughts

The learning curve of getting the Arduinos, laptops and components to talk to each other was incredibly steep. A few pointers from the ever-helpful Colette Matthewman helped immensely. Gratifyingly learning the XOD aspect of the project has been pretty straightforward. The online tutorials have stepped us through what we need to do in a logical manner.

 Our initial design has been modified, from just monitoring the height via the height sensor supplied, to attaching a Hall Sensor to the Arduino and attaching magnets to the hydrometer. We have developed ideas which can spring from this once we’ve got the basics in place and are quite excited (an overused word), about the potential scope of what we’re playing with.

 We are still very much in the early stages of the project, but are learning and have welcomed the opportunities to work towards a common goal (better beer), whilst acquiring new skills. This project has some way to run and will, no doubt, be adapted, modified and changed over time.

Follow our progress (intermittently) via twitter @dewhurst_ben, @popupcamptrout, @LP_Alwyn, @AutoBrewControl

More information about the Biomaker Challenge can be found at www.biomaker.org

[Closes 6 Jan 2019] Post-doctoral researcher position in the Osbourn Group at John Innes Centre

Closing Date: 6 Jan 2019

>>> Apply here <<<

Grade SC6 Starting Salary: £31,250 - £35,400

Expected/Ideal Start Date: 01 Feb 2019

Duration: 17 Months

Main Purpose of the Job

Applications are invited for a Postdoctoral Scientist with expertise in natural product chemistry. The post involves extraction, analysis, purification and structural determination of medicinally important complex triterpene glycosides . The successful candidate will work with other researchers within the Osbourn lab as part of a multi-disciplinary team.

Further details of this project and the laboratory can be found at https://www.jic.ac.uk/scientists/anne-osbourn/.

Key Relationships

The successful applicant will be line-managed by Professor Anne Osbourn. The position is one of four postdoctoral positions funded by a Biotechnology and Biological Sciences Research Council (BBSRC) Super Follow-on Fund award for translational research. The successful applicant will work closely with this team and with John Innes Centre Metabolite Services.

Main Activities & Responsibilities

• Extraction, analysis, purification and strutcural determination of complex triterpenes (saponins)

• Prepare results, reports and manuscripts for publication in leading scientific journals and other relevant media

• Disseminate research findings though presentations to various audiences at internal, national and international meetings

• Collaborate with colleagues within the Institute in the development of original and world-class research, including contributing to research proposals and grant applications

• Liaise with industry and other external stakeholders

• Ensure research and record keeping is carried out in accordance with good practice, Scientific Integrity and in compliance with local policies and any legal requirements

• Contribute to the smooth running of the group, including the effective use of resources, supervision of visitors to the laboratory and assisting with training others, encouraging scientific excellence

• Continually strive for excellence, seeking out and acting on feedback and relevant learning and development opportunities

As agreed with line manager, any other duties commensurate with the nature of the role

The Biomaker Challenge Winners and ways to get involved

The 2018 Summer Biomaker Challenge was wrapped up in October with a showcase event, but it not all over. Biomaker activities are still going strong! Below is a summary of activities as well as a write up of the Biomaker Fayre and the winning teams….

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Biomaker Activities

Winter Software Challenge (apply by 16 December 2018): Interested in programming? Low-cost hardware for science? Learning new skills with a team? We provide the hardware, you develop software nodes for integrating hardware with new graphical programming interface, XOD. More information at www.biomaker.org/apply-now - a quick, rolling application process so you can receive your kit and start playing ASAP!

Norwich Biomakers - An interdisciplinary network exploring the cross-over of biology with design, technology, engineering, electronics, software, art and much more. A place to learn about the latest technologies, share ideas and skills and shape projects. We meet up on a monthly basis.

Cambridge Synthetic Biology meetups - A clearing house for a wide variety of regular open meetings like Cafe Synthetique, Science Makers and the SRI Forums - with a particular focus on building tools and interdisciplinary research.

Cambridge Biomakespace - Scientists, engineers, students and entrepreneurs are developing the new Cambridge Biomakespace - an innovation space for building with biology in the historic MRC Laboratory of Molecular Biology building.

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The Biomaker Fayre

On Saturday 29 October, over 100 attendees came together in the University of Cambridge Department of Engineering to showcase and celebrate open-source technologies in research and education. The day consisted of a morning of talks followed by the Biomaker Fayre, where this year's ten Biomaker Challenge teams exhibited their projects alongside industry leaders and independent makers.

We started the day with some inspiring talks: Paolo Bombelli & Alasdair Davies on open tools for animal conservation and the "Powered by Plants" project, Grey Christoforo on hacking 3D printers to create better solar cells, Helene Steiner on OpenCell and teaching the next generation of designers to work with scientists, Richard Hayler on citizen science and education with Raspberry Pi and Julian Stirling on open instrumentation for Africa.

After a coffee break and lunch, we headed upstairs for the Biomaker Fayre. There was a festive feel to the space- gold balloons marked each exhibit, 3D-printed trophies were on display to be given out at the end of day, and attendees filled the space, excited to get involved and try out some hands-on demos.

Exhibits covered everything from a cartesian coordinate robot for dispensing fruit fly food to a wearable biosensor for monitoring vaginal discharge and a temperature-controlled container for sample transportation. Among the exhibitors were the ten Biomaker Challenge teams. In June, each team were given a £1000 grant and four months to turn their ideas for open source and DIY research tools into a reality.

The Biomaker Challenge judges were very impressed by each one of the projects and ended up deliberating for over an hour. In the end, the 3D-printed trophies (low-cost and DIY of course) were presented to the following teams:

Best Technology

Dual-View Imaging in a Custom-Built Light Sheet Microscope

Stephanie Hohn, Hannah Sleath, Rashid Khashiev, Francesco Boselli, Karen Lee

"The large variety of Biomaker projects was very inspiring. We had a lot of fun during the challenge and the feedback from people in different fields was really helpful. It was great to get in touch with programmers, engineers and designers. We received a great confidence boost for future more technical projects."

Stephanie Hohn (University of Cambridge)

Best Biology

Spectre, Low-cost whole-cell biosensors for environmental and medical surveillance.

Feng Geng, Boon Lim, Xiaoyu Chen, Jimmy Chen

"The Biomaker Challenge has provided us a great opportunity to extend our research into real-world application. As most of us come from a biological background, we faced a lot of difficulties on assembling the electronics and programming our Arduino kit. With three months of perseverance and constant guidance from our advisor Tony, we managed to come up with a customised, miniaturised spectrophotometer which can be used in conjunction with our whole-cell biosensor. We received an Arduino kit and sufficient funding to get us through the proof-of-concept stage of our project and from here, we are planning to further develop and optimise our device into a start-up company. It is amazing to think that it all starts with a small Biomaker Challenge Summer Project!"

Boon Lim, University of Oxford

Maker Spirit

Wearable biosensor for monitoring vaginal discharge

Tommaso Busolo, Giulia Tomasello, Michael Calabrese, James Che

"We all really enjoyed the multidisciplinary nature of the challenge, working with people from all sorts of backgrounds. We feel we now have a much clearer, hands-on insight into how the more diverse a collaboration is, the more relevant, impactful and exciting the results of ideas brainstorming can be!"

Michael Calabrese, University of Cambridge

Biomaker Challenge and Open Technology Workshop aimed to show the value of open, low-cost and DIY technologies as convening points for interactions between biologists and engineers. They are also important educational tools for those who are interested in developing technical skills and have great potential for improving the quality of science and increasing productivity in the lab for lower costs. With the proliferation of digital designs for 3D-printing and easily available consumer electronics like Arduino which has a huge community of users and lots of online help, designing your instrumentation around your experiment rather than vice versa has never been more possible.

Check out more photos from the day!

The descriptions of all prototypes are available at www.hackster.io/biomaker. To find out more about the most recent and upcoming competitions go to www.biomaker.org/biomaker-challenge to be kept up to date​​​​​​ with developments.

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Biomaker Challenge 2018 was funded by OpenPlant, a BBSRC/EPSRC Synthetic Biology Research Centre Grant BB/L014130/1. The Biomaker Challenge and Open Technology Workshop were coordinated by University of Cambridge's Synthetic Biology Strategic Research Initiative

Late night (biological) engineering in London

By Sami Stebbings

Once a month something amazing happens at the London Science Museum, and last month our collaborative team from OpenPlant, the SAW Trust, the University of East Anglia (UEA) and graphic recorder Rebecca Osborne, got to be part of it.

On the last Wednesday of every month, the London Science Museum opens its doors late into the evening to welcome adults to an engaging and free evening out, as part of the Science Museum Lates.

Each evening is themed around a different science topic, attracts around 4,000 guests per night and offers a relaxed atmosphere where you can walk around with a drink in hand whilst talking science.

This month’s theme was ‘The year of the engineer’ and we brought the synthetic biology edge to the night with our ‘Engineering Natural Products’ stand. With the help of Dr Richard Bowater (University of East Anglia), Hannah Griffiths (John Innes Centre) and of course DNA Dave, visitors were taken on a journey from the discovery of DNA through to how scientists engineer biological systems.

Our enthusiastic public engagement volunteers, Jenni Rant and Sami Stebbings (SAW Trust) and John Innes Centre PhD students' Hannah Griffiths and Shannon Woodhouse.

Our stand told the story of avenacin, a triterpene that is found in the roots of oat plants and helps make the plant resistant to fungal diseases. By understanding how these plants produce avenacin from the instruction in their DNA, we explored how scientists can engineer other biological systems to mimic their production. For example, can we transfer these genes from oat plants, into other crops, such as wheat which have no natural antifungal protection?

Guests had a plethora of activities to take part in, from our ‘Fishing for DNA’ activity, Avenacin Pathway puzzle, to getting up close and personal with an avenacin molecule using VR. They also had a chance to get hands on and infiltrate tobacco plants and see fluorescing oat seedlings!

With a steady stream of people throughout the night, the evening was a great success (not only because there was gin bar)! A massive thank you to all our collaborators who helped pull our stand and activities together, as well as the fantastically organised, London Science Museum team.

In was a great event to be part of and we hope to return to another Lates event sometime in the future!

OpenPlant Forum 2018: Engineering Plants for Bioproduction

Blog post by Dr Colette Matthewman

Over the past decade, synthetic biology has focussed much of its effort on microbial chassis as platform for bioproduction. The single cell simplicity and rapid life-cycles of these organisms, the prevalence of biological tools and the existing industry infrastructure for fermentation have made microbes a tempting playground for synthetic biologists wishing to make a range of chemicals and biomolecules, from flavours and fragrances to distributed manufacturing of highly complex metabolites for medicine, and an increasing number of companies are finding success in this arena (e.g. Ginkgo Bioworks, Amyris, Evolva, Antheia).

More recently, plants have been showing serious promise as viable production platforms for complex chemicals and biomolecules which in many cases simply can’t be made in single celled microbes. This year, the OpenPlant Forum explored some of the latest advances in plant bioproduction with inspiring talks from invited speakers and OpenPlant researchers highlighting a promising and exciting future for plant synthetic biology.

OpenPlant post-doc Ingo Appelhagen presents his work on anthocyanin pigment production in plant cell cultures.

The first morning of the Forum focused on tools for refactoring regulation and simple test platforms for plant synthetic biology. Prof. Ian Small (University of Western Australia) opened the meeting with a keynote on the potential for using engineered RNA bonding proteins to control organelle gene expression. OpenPlant PI, Prof. Paul Dupree described research in his on engineering of polysaccharide structures in plants. We also had the first examples of plant production platforms: Dr Ingo Appelhagen presented his recently published work on the production of colourful anthocyanin molecules in plant cell cultures, while Dr Eva Thuenemann introduced the HyperTrans system developed in the Lomonossoff lab at the John Innes Centre for the transient expression of proteins in Nicotiana benthamiana, a wild relative of tobacco. Eva is working on plant-based production of a protein that could be used in a vaccine against East Coast Fever, a devastating disease in cattle in Africa. The HyperTrans platform is used by the Lomonossoff lab and recently established company Leaf Expression Systems to produce therapeutic proteins and virus-like particles for vaccines, including recent work on a new vaccine for the eradication of Polio.

The afternoon session explored the cutting edge in production of complex plant-derived natural products in yeast, with a keynote from Prof. Christina Smolke (Stanford University), followed with an insight into the engineering of triterpene production in N. benthamiana by Dr James Reed in the Osbourn lab (John Innes Centre), recently reviewed in Plant Cell Reports. These projects rely heavily on chemical and enzymatic biodiversity in nature. Dr Sam Brockington (University of Cambridge) talked about harnessing the global network of botanic gardens for access to plant diversity for metabolic engineering and synthetic biology, introducing a global database of living plant, seed and tissue collections called “Plant Search” – a perfect sedgeway into a panel discussion on Harnessing Global Biodiversity where Sam was joined by Dr Nicola Patron (Earlham Institute), Mr David Rejeski (Environmental Law Institute), and Dr Jenni Rant (SAW Trust). The discussions ranged from public opinion on synthetic biology (explored through the Global Garden workshop) and benefit sharing and dematerialisation, through to how blockchain (like the bitcoin) is being used in environmental contexts and whether blockchain technology trends can be applied to create/assign value for biodiversity.

Prof. Ralf Reski with his moss bioreactors

Day two of the Forum continued on a theme of “Tools for Metabolic Engineering” with Prof. Claudia Vickers (University of Queensland) opening by introducing the Future Science Platform in Synthetic Biology that she leads at CSIRO, as well as numerous tools developed in her research lab. Claudia was followed by a trio of OpenPlant postdocs describing analysis to unravel the genetics of divergent metabolic pathways in Brassicaceae (Dr Zhenhua Liu), a search for new synthetic biology tools based on diversity of natural triterpene oxidation (Dr Michael Stephenson) and tools for engineering Marchantia’s chloroplasts (Dr Eftychis Frangedakis).

Moving on from the tools, we explored further plant-based bioproduction platforms, starting with an inspirational keynote from Prof. Ralf Reski (University of Freiburg) on the moss Physcomitrella patens that Ralf’s lab has established as a production platform for biopharmaceuticals, leading to foundation of the company Greenovation, which produces moss-aGal (agalsidase) for the treatment of Fabry disease, a rare but painful and potentially deadly disease. Subsequently, we heard from Prof. Alison Smith (University of Cambrige) about “Designer algae” and work towards predictable metabolic engineering in microalgae, and from Dr Eugenio Butelli (John Innes Centre) about the Tomato as a biofactory for making health promoting flavonoids.

The Forum was wrapped up for this year with a session on Sharing and Techno-Social Platforms, with an introduction from OpenPlant’s Prof Jim Haseloff, followed by Dr Linda Kahl (BioBricks Foundation) on the latest with the Open Material Transfer Agreement (Open MTA) which has been developed in collaboration with OpenPlant to enable sharing of DNA parts (publication coming soon!). Next up, Dr Joanne Kamens from not-for-profit plasmid distribution company, Addgene, revealed the freshly launched plant resource page and spoke about the upcoming adoption of the Open MTA as an option under which plasmids can be shared. Finally, Dr Richard Sever from bioRxiv spoke about preprint opportunities for synthetic biology.

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Join us in Cambridge for the OpenPlant Forum 2019 | 29 – 31 July

Save the date!

[Closes 14 September 2018] Technologist in DNA packaging and delivery in Edinburgh

This position is within Prof Alistair Elfick lab, School of Engineering and UK Centre for Mammalian Synthetic Biology (www.synbio.ed.ac.uk) 

The Role:

An important underpinning technology for synthetic biology is the synthesis of DNA. Technology has now advanced to the point where it is possible to affordably construct very large constructs up to chromosome scale. An emergent bottleneck is the delivery of this into the cell. The Technologist will be actively involved in contributing to the standard development programme of the UK Centre for Mammalian Synthetic Biology (UK-CMSB), in collaboration with the National Physical Laboratory. They will be primarily responsible for delivering technologies to achieve the packaging and non-viral delivery of large DNA constructs into mammalian cells, with their reduction to practise as standard protocols. Their secondary role is the support of collaboration with academic and research staff and students of the UK-CMSB. The post holder will ensure that the development of UK-CMSB technology standards supports and keeps pace with the research requirements, liaising with industry, collaborators and users, advising and training staff and students.

Fixed term for 2 years

Grade 7

Closing date Sept 14th 2018

Vacancy reference www.vacancies.ed.ac.uk  search for #044849

Contact Alistair.elfick@ed.ac.uk for further information

The Mad Hatter's Tea-party at Boomtown

Following last year’s success at BoomTown Fair, we returned, alongside the SAW Trust, with an Alice In Wonderland themed delight for the senses, with science, art and writing activities to excite young minds.

Table laid and ready for the first guests to arrive!

Now in its tenth year, BoomTown Fair attracts up to 60, 000 people and many of those came to visit us at Kidztown, with its impressive visual displays and interactive activities for families. 

Our stand entitled “The Mad Hatter’s Tea Party” revolved around workshops which had four stations for the children to rotate around. The tea parties began with the mad hatter revealing secret invisible ink messages to the children before the experiments could begin!

The children were tasked with many exciting science-based activities. Tasty treats the children could create included sweet, fizzy sherbet and rapid ice-cream made using an endothermic reaction and flavoured with plant flavourings (vanilla, coconut and strawberry). In addition to these, there were also many pigment-based activities inspired by all the bright colours in Wonderland, for the children to try. Including; natural plant pigment tissue tie-dyes and colour changing flowers and celery. The results of which decorated the tent throughout the weekend.

Carrying on with our use of plant products, the children also got to create their own fruit flavoured jelly balls, using alginate gelling agent, derived from algae, to go with a fizzy drink!

The final activity for the children was to write secret messages, which would be revealed by a new set of children, at the next tea party by the Mad Hatter.

Some of our tea-party guests about to make sweet treats.

As well as the tea parties, there were also numerous activities and challenges for the children to engage with while the table was re-set. These activities included using microscopes to explore the microscopic world Alice enters when she shrinks, writing nonsense poems, like those the Mad Hatter recites at his tea party and pinning the grin on the Cheshire cat.

We had a range of craft activities available, providing the children with something to take home with them from their time at BoomTown. The children could make Wonderland inspired flower faces, clock necklaces, a Mad Hatter’s Hat and playing card bowties.

Across the three days the children were able to immerse themselves in a Wonderland of science, art and writing, feeding their curiosity with a range of thrilling experiments and allowing their creativity to run wild with exciting craft projects.

A big thank you to the entire team who helped with the preparations and running of “The Mad Hatters Tea Party” and to BoomTown for having us once again!

By Shannon Woodhouse

An internship with the SynBio 4 Schools project

PhD student Camilla Stanton spent a three month internship, from May to August 2018, working with OpenPlant to build resources and materials for the Synthetic Biology for Schools (SynBio4Schools) project, funded through the OpenPlant Fund scheme. In this blog post she describes the project and the work that she completed during her placement.

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Synthetic biology brings together researchers from a broad range of backgrounds to solve biological problems through rational design. While synthetic biology is increasingly being taught in universities, it remains under-represented in the national curriculum and teaching resources for GCSE and A-Level students. The SynBio 4 Schools project aims to solve this problem by creating a comprehensive educational resource package that teaches the principles of plant synthetic biology through practicals and case studies.

SynBio4Schools activites and write-ups on display at the OpenPlant Forum, Norwich, 2018

I got involved with the SynBio 4 Schools project through a 3-month industrial placement as part of my PhD. My role was to assess and identify what resources could be included and to begin compiling them. An obvious starting place was to explore the activities and demonstrations that researchers in Norwich and Cambridge had already developed and tested. While these resources are valuable on their own, bringing them together creates a set of interlinked resources that support one another, greatly increasing their reach and impact. It is also an exciting opportunity to get contemporary research into schools, helping inspire the next generation of biological engineers!

During my placement, I worked in collaboration with researchers to discuss ideas for how their research could be used in a teaching-style activity, whether that be an experiment, worksheet or craft-based. We also had discussions about what sort of supporting material might be useful, such as articles, interviews or case studies. It was a really enjoyable process as it gave the scientists a unique opportunity to think more creatively about their work, and I got to hear some really innovative ideas for teaching some quite complex concepts.

Some of the 3D printed virus structures from Roger Castells-Graells' OpenPant Fund Project.

I ended up focussing on writing up three activities based on work carried out by Dr Paolo Bombelli (plant microbial fuel cells), Dr Nicola Patron (genetic circuits) and Roger Castells-Graells (virus structures), which I was lucky enough to showcase at the OpenPlant Forum. This gave me the chance to receive feedback from other researchers and educators about how the materials could be made more accessible for students and provide more support for teachers and technicians. These suggestions helped shape the basic write-up template, which now includes additional investigations, sources and links to other experiments. 

This was a hugely valuable experience for me - I got to explore new topics, meet people with exciting and original ideas and even got to try my hand at some design work! Although I’m now back doing my PhD, the SynBio 4 Schools project definitely doesn’t end there - we want as many people as possible to get involved.

Currently, there is a growing list of activities that cover a variety of topics from plant natural products to computational biology. But we want to showcase even more research from Norwich and Cambridge! If you have developed a resource that you would like to see included in the SynBio 4 Schools project, or you think your research could translate into an educational setting, please do get in touch! Email Colette.Matthewman@jic.ac.uk

MRes Biotechnology and Biodesign

University of Newcastle are offering a new MSc program in Biotechnology and Biodesign. The course provides a foundation into how design and engineering approaches are used in the creation of new biotechnological processes and products.

More information and to apply>>>

About this course

Advances in biotechnology, computing, and laboratory automation are being coupled with design thinking approaches to engineer biological systems that may produce more sustainable products than traditional manufacturing. Examples include:

• the production of synthetic meat substitutes
• dairy-free milk
• adaptive building materials
• petroleum-replacement products
• designer antimicrobial compounds
• smart drug delivery systems

Our Biotechnology and Biodesign MRes:

• provides a foundation in design thinking approaches
• covers recent developments in applied biotechnology
• provides an opportunity to develop and refine your laboratory skills
• provides the opportunity to develop your own research project

The training forms an excellent foundation for students opting to follow a research orientated career path and for those looking for successful careers in the biotechnology industry.

The course is interdisciplinary. You'll be suitable for this course if you are:

• a science graduate
• looking to develop your knowledge and research skills

You'll gain the skills allowing you to address critical global challenges in:

• sustainability
• food security
• the environment
• healthcare

[Closes 30 May 2018] Co-ordinator for Synthetic Biology Centre

We're looking to hire a Cambridge-based coordinator for the OpenPlant SynBio Research Centre and the Cambridge SynBio Strategic Research Initiative. Application deadline is 30 May 2018.

Full details of the post can be found at http://www.jobs.cam.ac.uk/job/17351/

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The role-holder would work 50% to support the OpenPlant Synthetic Biology Research Centre and 50% with the Synthetic Biology Strategic Research Initiative (SynBio SRI). The purpose of the role is to help develop and implement a strategy that will enable both initiatives to become known leaders in the field and sustainable in the longer term.

OpenPlant (http://openplant.org) is a consortium funded by BBSRC and EPSRC comprising 20 labs spanning the University of Cambridge, John Innes Centre and the Earlham Institute (Norwich). The work of the Research Centre is intended to promote novel research on tools and applied traits for plant synthetic biology, open sharing of foundational technologies, and responsible innovation. The role-holder will work with the OpenPlant Directors and Management Group, including the OpenPlant Project Manager based in Norwich, to co-ordinate a variety of activities within the Research Centre.

The SynBio SRI (http://synbio.cam.ac.uk) aims to catalyse interdisciplinary exchange between engineering, physics, biology and social sciences to advance Synthetic Biology at the University of Cambridge. The role-holder will work with the SRI Co-Chairs and Steering Committee to develop, plan and deliver the SRI's vision and strategy. They will facilitate efforts to promote development of open technologies, build shared resources, and provide a hub for networking and discussion.

Responsibilities will also include co-ordinating seed funding competitions such as the Biomaker Challenge and OpenPlant Fund; organising formal and informal scientific meetings and forums; developing and managing relationships with stakeholders within and external to the University; seeking small and large-scale funding for future activities. The role-holder is additionally responsible for ensuring that synthetic biology activities in Cambridge are actively communicated and promoted, and is supported by the part-time SynBio SRI Events and Communication Co-ordinator.

The successful candidate will have a PhD in a relevant field and knowledge of Synthetic Biology research, policy and practice. They will have the ability to foster relationships with and between academics at all levels in an interdisciplinary context, and build partnerships with companies, funders and policy makers. A successful track record in attracting research funding would be advantageous. Excellent organisational and communications skills are essential, together with proven problem-solving skills and initiative.

Fixed-term: The funds for this post are available until 30 September 2019 in the first instance.

Cell-free protein synthesis - try it with your favourite protein!

Quentin Dudley, a postdoc at the Earlham Institute, did a PhD in the Jewett lab (Northwestern University, Illinois) focused on the use of cell-free systems for the reconstitution of metabolic pathways and bioproduction of monoterpenes. Now he is using an OpenPlant Fund Award to establish cell-free platforms for protein synthesis in Norwich. Read more about this work below, and on www.biomaker.org

As part of this project he is recruiting participants for a workshop on cell-free protein synthesis to be held in mid-June in Norwich. It is an opportunity to try to express your favourite protein using a low-cost, high-throughput platform. Download the poster for details and contact quentin.dudley@earlham.ac.uk for details and questions.

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Cell-free protein synthesis

Cell-free protein synthesis (CFPS) uses crude lysates of E. coli, wheat germ, and other organisms to recapitulate transcription and translation in a test tube (Carlson et al., 2012). This enables protein production at higher throughput, shorter timescales, and simpler troubleshooting compared to expression in cells. While CFPS has several pros/cons, it is particularly powerful when testing many different protein variants/mutations with an output assay that works directly in the crude cell-free reaction.

While CFPS is getting easier to implement, buying commercial kits can get expensive and troubleshooting the first time can be challenging. In response, I’m leading a project sponsored by the OpenPlant fund to establish an in-house E. coli CFPS system (~£1 / rxn) at Norwich/Cambridge and want to compare it to a commercial wheat germ kit (£12 / rxn) for expressing proteins. We are testing a range of different proteins from various plants. If you have an interesting protein you’d like to try expressing in a cell-free system, please contact quentin.dudley@earlham.ac.uk for details!)

I’ve previously worked with CFPS as a graduate student with Michael Jewett at Northwestern University. The Jewett lab is working to develop new CFPS platforms using yeast (S. cerevisiae), chloroplasts, and CHO cells. They also are improving existing E. coli-based systems to synthesize “tricky” proteins that require complex folding environments (membrane proteins, antibodies) or contain nonstandard amino acids. During my time in the lab, I used CFPS to manufacture enzyme homologs which could then be combined to prototype metabolic pathways, for example biosynthesis of monoterpenoids.

It is a very exciting time for cell-free systems. Protein yields have increased to 2 mg/mL and a commercial company (Sutro Biopharma) has reported reaction volumes at 100 L (Zawada et al., 2011). Additionally, cell-free reactions can be freeze-dried on paper and retain full activity; several groups are using this feature to develop on-demand pharmaceuticals or simple, color-changing diagnostics for diseases such as Zika virus (Pardee et al., 2016). As this cell-free technology matures, its flexibility and programmability make it an attractive opportunity for Biomaker projects and future applications will be limited only by the creativity of researchers and developers.

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REFERENCES

Carlson, E. D., Gan, R., Hodgman, C. E., & Jewett, M. C. (2012). Cell-free protein synthesis: applications come of age. Biotechnology Advances, 30(5), 1185-1194.

Zawada, J. F., Yin, G., Steiner, A. R., Yang, J., Naresh, A., Roy, S. M., ... & Murray, C. J. (2011). Microscale to manufacturing scale‐up of cell‐free cytokine production—a new approach for shortening protein production development timelines. Biotechnology and Bioengineering, 108(7), 1570-1578.

Pardee, K., Green, A. A., Takahashi, M. K., Braff, D., Lambert, G., Lee, J. W., ... & Collins, J.J. (2016). Rapid, low-cost detection of Zika virus using programmable biomolecular components. Cell, 165(5), 1255-1266.